Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for PNLIPRP2
Basic gene info.Gene symbolPNLIPRP2
Gene namepancreatic lipase-related protein 2
SynonymsPLRP2
CytomapUCSC genome browser: 10q25.3
Genomic locationchr10 :118380464-118404654
Type of geneprotein-coding
RefGenesNM_005396.4,
NR_103727.1,
Ensembl idENSG00000266200
DescriptionPL-RP2galactolipase
Modification date20141207
dbXrefs MIM : 604423
HGNC : HGNC
Ensembl : ENSG00000266200
HPRD : 05110
Vega : OTTHUMG00000181599
ProteinUniProt: P54317
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PNLIPRP2
BioGPS: 5408
Gene Expression Atlas: ENSG00000266200
The Human Protein Atlas: ENSG00000266200
PathwayNCI Pathway Interaction Database: PNLIPRP2
KEGG: PNLIPRP2
REACTOME: PNLIPRP2
ConsensusPathDB
Pathway Commons: PNLIPRP2
MetabolismMetaCyc: PNLIPRP2
HUMANCyc: PNLIPRP2
RegulationEnsembl's Regulation: ENSG00000266200
miRBase: chr10 :118,380,464-118,404,654
TargetScan: NM_005396
cisRED: ENSG00000266200
ContextiHOP: PNLIPRP2
cancer metabolism search in PubMed: PNLIPRP2
UCL Cancer Institute: PNLIPRP2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PNLIPRP2 in cancer cell metabolism1. Zhang G, He P, Tan H, Budhu A, Gaedcke J, et al. (2013) Integration of metabolomics and transcriptomics revealed a fatty acid network exerting growth inhibitory effects in human pancreatic cancer. Clinical cancer research 19: 4983-4993. go to article

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Phenotypic Information for PNLIPRP2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PNLIPRP2
Familial Cancer Database: PNLIPRP2
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
KEGG_GLYCEROLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 604423; gene.
Orphanet
DiseaseKEGG Disease: PNLIPRP2
MedGen: PNLIPRP2 (Human Medical Genetics with Condition)
ClinVar: PNLIPRP2
PhenotypeMGI: PNLIPRP2 (International Mouse Phenotyping Consortium)
PhenomicDB: PNLIPRP2

Mutations for PNLIPRP2
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PNLIPRP2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=31)
Stat. for Synonymous SNVs
(# total SNVs=16)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr10:118386478-118386478p.A145V3
chr10:118396421-118396421p.F354F2
chr10:118404581-118404581p.N460N2
chr10:118385499-118385499p.F83I2
chr10:118386491-118386491p.F149L2
chr10:118404543-118404543p.?2
chr10:118383592-118383592p.E62E1
chr10:118390843-118390843p.I264I1
chr10:118386379-118386379p.M112K1
chr10:118389458-118389458p.L194L1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=0

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample                    
# mutation                    
nonsynonymous SNV                    
synonymous SNV                    
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for PNLIPRP2 in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for PNLIPRP2

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

B3GNT1,C4BPB,LRRC73,TMEM244,CFC1B,DRAP1,FAM155A,
FAM74A3,GOLT1A,HSPA12A,INPP5J,KRTAP10-8,MSRB2,MT3,
OR4K1,PELI3,PNLIPRP2,RANGRF,SERGEF,SIRT3,TM7SF2
AKAP5,ASTL,BNIPL,DCT,DYTN,ESR1,FAM47A,
FGF3,IGDCC3,KRTAP5-8,LUZP2,NCAM2,NDP,OR4M1,
PNLIPRP2,POF1B,SMCP,SPATA19,SPOCK3,SULT1E1,WNT5A

ABCC6P2,ACSS2,CPA2,DDC,DHRS11,DUSP15,TMEM236,
GLOD5,GOLGA6L6,GSS,MMEL1,SLC51B,PNLIPRP1,PNLIPRP2,
PNPLA1,PXMP4,SEPHS2,SHOX,SLC13A2,SLC23A1,SLC3A1
ALDOC,AQP3,CCDC108,CREB3L3,DNASE1,F11,GPR112,
KCNH6,KCNJ3,MLXIPL,MUC17,NR0B2,PFKFB4,PLB1,
PNLIP,PNLIPRP2,PRODH,REEP6,SI,VNN1,ZNF488
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for PNLIPRP2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL2169728; -.
Organism-specific databasesPharmGKB PA33480; -.
Organism-specific databasesCTD 5408; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02613pancreatic lipase-related protein 2experimentalDecylamine-N,N-Dimethyl-N-Oxide


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Cross referenced IDs for PNLIPRP2
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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